When working with coarse-grained (CG) molecular dynamics simulations, one common scenario is modeling systems that contain multiple copies—or replicas—of the same protein. This is typical in studies involving protein aggregation, crowding effects, or multi-component assemblies using approaches like the MARTINI force field. However, many users face a recurring technical challenge: topology errors due to chain and residue ID conflicts.
If you’re using the Martinize2 Extension in SAMSON, ensuring that each chain and residue in your replicated system has a unique ID is critical before generating CG models. In this post, we walk through the key steps to properly manage replicas and prevent errors before they arise.
Why unique numbering matters
GROMACS and similar molecular dynamics tools expect unambiguous identifiers for residues and chains. If your system contains multiple chains with overlapping residue numbers or identical chain names, you can run into problems when creating topology files. Martinize2 requires that each chain and residue be properly distinguished.
How to renumber replicas in SAMSON
Once you’ve created your protein replicas—either manually, via scripting, or using the Molecular Box Builder—the next step is to make them distinguishable. Here’s how you do that:
1. Renumber residue IDs
Right-click the structural model in the document view and select:
Structural model > Renumber residues and structural groups
In the dialog that opens, leave the default starting value as 1 and press OK.
2. Renumber chain IDs
Next, ensure each chain has a unique identifier:
Right-click the structural model again and choose:
Structural model > Renumber chain IDs
Specify the starting ID (keep it at 0 for automatic) and click OK.
3. Rename chains (optional but helpful)
To keep your document organized, you can give each chain a unique name. Select a chain and press F2, or right-click and choose Rename:
This can also be done through the Inspector interface:
Next step: Generate CG models
Once your replicas are uniquely numbered and named, you can proceed to generate coarse-grained models just like you would for a single structure. Open the Martinize2 extension, set your system, configure parameters as needed, and click Create coarse-grained models.
This preparation step often saves hours of debugging and ensures that the topology files generated for GROMACS run smoothly without modifications.
To learn more, head over to the full Martinize2 tutorial in the SAMSON documentation: https://documentation.samson-connect.net/tutorials/martinize2/martinize2/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.